rs79218129
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_139280.4(ORMDL3):c.-22-292C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00854 in 152,270 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0085 ( 12 hom., cov: 32)
Consequence
ORMDL3
NM_139280.4 intron
NM_139280.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0760
Genes affected
ORMDL3 (HGNC:16038): (ORMDL sphingolipid biosynthesis regulator 3) Involved in ceramide metabolic process. Acts upstream of or within several processes, including negative regulation of B cell apoptotic process; negative regulation of ceramide biosynthetic process; and positive regulation of protein localization to nucleus. Located in endoplasmic reticulum. Part of SPOTS complex. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00854 (1300/152270) while in subpopulation AFR AF= 0.0297 (1233/41546). AF 95% confidence interval is 0.0283. There are 12 homozygotes in gnomad4. There are 615 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1300 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ORMDL3 | NM_139280.4 | c.-22-292C>T | intron_variant | ENST00000304046.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ORMDL3 | ENST00000304046.7 | c.-22-292C>T | intron_variant | 1 | NM_139280.4 | P1 | |||
ORMDL3 | ENST00000579695.5 | c.-17-297C>T | intron_variant | 1 | P1 | ||||
ORMDL3 | ENST00000394169.5 | c.-23+238C>T | intron_variant | 2 | P1 | ||||
ORMDL3 | ENST00000584000.1 | c.-22-292C>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00856 AC: 1302AN: 152152Hom.: 12 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1302
AN:
152152
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00854 AC: 1300AN: 152270Hom.: 12 Cov.: 32 AF XY: 0.00826 AC XY: 615AN XY: 74456
GnomAD4 genome
?
AF:
AC:
1300
AN:
152270
Hom.:
Cov.:
32
AF XY:
AC XY:
615
AN XY:
74456
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
5
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at